Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013913.1 Corchorus capsularis cultivar CVL-1 contig13934, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 31922
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:2548 original size:19 final size:18

Alignment explanation


    Indices: 2515--2550  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2505 TTGAAATAAT

                              
       2515 TCTTCAATAATCTTCAAA
          1 TCTTCAATAATCTTCAAA

                     *        
       2533 TCTTCAAATTATCTTCAA
          1 TCTTC-AATAATCTTCAA

       2551 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42


Consensus pattern (18 bp):   
TCTTCAATAATCTTCAAA

Found at i:4765 original size:13 final size:13

Alignment explanation


    Indices: 4747--4780  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       4737 TCGAAATTTG

                         
       4747 AAGAAAAAGAAAA
          1 AAGAAAAAGAAAA

                         
       4760 AAGAAAAAGAAAA
          1 AAGAAAAAGAAAA

             *      
       4773 ATGAAAAA
          1 AAGAAAAA

       4781 AATGAAAAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03


Consensus pattern (13 bp):   
AAGAAAAAGAAAA

Found at i:4789 original size:7 final size:6

Alignment explanation


    Indices: 4747--4780  Score: 50
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       4737 TCGAAATTTG

                                                   
       4747 AAGAAA AAGAAAA AAGAAA AAGAAA AATGAAA AA
          1 AAGAAA AAG-AAA AAGAAA AAGAAA AA-GAAA AA

       4781 AATGAAAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
   6   14  0.54
   7   12  0.46

ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03


Consensus pattern (6 bp):   
AAGAAA

Found at i:22758 original size:30 final size:30

Alignment explanation


    Indices: 22717--22782  Score: 78
    Period size: 30  Copynumber: 2.2  Consensus size: 30

      22707 AAAGGGTCAA

                                 *        
      22717 ATGGCCGGTTGTGCCCGGATGGTCCATGCG
          1 ATGGCCGGTTGTGCCCGGATGCTCCATGCG

                *        *    *        *  
      22747 ATGGGCGGTTGTGGCCGGTTGCTCCATCCG
          1 ATGGCCGGTTGTGCCCGGATGCTCCATGCG

            *     
      22777 TTGGCC
          1 ATGGCC

      22783 CATGCGATGG


Statistics
Matches: 29,  Mismatches: 7, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.08, C:0.27, G:0.39, T:0.26


Consensus pattern (30 bp):   
ATGGCCGGTTGTGCCCGGATGCTCCATGCG

Found at i:24197 original size:68 final size:68

Alignment explanation


    Indices: 24104--24236  Score: 187
    Period size: 68  Copynumber: 2.0  Consensus size: 68

      24094 TCTCTCTGTT

                                        *                **        *    *    
      24104 TTTTTTTTTCCAAAGGGAAAACTCTTGGGAATTTACTAAATTCACTGATGTCTCTTCTCCTCTTT
          1 TTTTTTTTTCCAAAGGGAAAACTCTTGGAAATTTACTAAATTCACCAATGTCTCTCCTCCCCTTT

               
      24169 TAC
         66 TAC

                          *    *                                             
      24172 TTTTTTTTT-CAAGGGGGACAACTCTTGGAAATTTACTAAATTCACCAATGTCTCTCCTCCCCTT
          1 TTTTTTTTTCCAA-AGGGAAAACTCTTGGAAATTTACTAAATTCACCAATGTCTCTCCTCCCCTT

             
      24236 T
         65 T

      24237 ATTTCACTTT


Statistics
Matches: 57,  Mismatches: 7, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  67    3  0.05
  68   54  0.95

ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42


Consensus pattern (68 bp):   
TTTTTTTTTCCAAAGGGAAAACTCTTGGAAATTTACTAAATTCACCAATGTCTCTCCTCCCCTTT
TAC
Done.